From c891831890341ad2859f15746803395cbb675816 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Wed, 23 Jan 2013 10:51:13 +0000 Subject: sci-biology/samtools: Drop old; use pkg-config to check for libncurses (Portage version: 2.2.0_alpha159/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916) --- sci-biology/samtools/ChangeLog | 11 +++++- sci-biology/samtools/metadata.xml | 10 ++--- sci-biology/samtools/samtools-0.1.12a-r1.ebuild | 47 ---------------------- sci-biology/samtools/samtools-0.1.16.ebuild | 47 ---------------------- sci-biology/samtools/samtools-0.1.17.ebuild | 48 ----------------------- sci-biology/samtools/samtools-0.1.18-r1.ebuild | 52 +++++++++++++++++++++++++ 6 files changed, 66 insertions(+), 149 deletions(-) delete mode 100644 sci-biology/samtools/samtools-0.1.12a-r1.ebuild delete mode 100644 sci-biology/samtools/samtools-0.1.16.ebuild delete mode 100644 sci-biology/samtools/samtools-0.1.17.ebuild create mode 100644 sci-biology/samtools/samtools-0.1.18-r1.ebuild (limited to 'sci-biology') diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog index bafb11674633..3b5f84fde598 100644 --- a/sci-biology/samtools/ChangeLog +++ b/sci-biology/samtools/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/samtools -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.8 2011/09/26 15:18:39 weaver Exp $ +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.9 2013/01/23 10:51:13 jlec Exp $ + +*samtools-0.1.18-r1 (23 Jan 2013) + + 23 Jan 2013; Justin Lecher -samtools-0.1.12a-r1.ebuild, + -samtools-0.1.16.ebuild, -samtools-0.1.17.ebuild, +samtools-0.1.18-r1.ebuild, + metadata.xml: + Drop old; use pkg-config to check for libncurses *samtools-0.1.18 (26 Sep 2011) diff --git a/sci-biology/samtools/metadata.xml b/sci-biology/samtools/metadata.xml index 3302123e5718..fc7c76942a10 100644 --- a/sci-biology/samtools/metadata.xml +++ b/sci-biology/samtools/metadata.xml @@ -1,9 +1,9 @@ - - weaver@gentoo.org - Andrey Kislyuk - - sci-biology + + weaver@gentoo.org + Andrey Kislyuk + + sci-biology diff --git a/sci-biology/samtools/samtools-0.1.12a-r1.ebuild b/sci-biology/samtools/samtools-0.1.12a-r1.ebuild deleted file mode 100644 index 5c689a266cee..000000000000 --- a/sci-biology/samtools/samtools-0.1.12a-r1.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12a-r1.ebuild,v 1.3 2011/07/18 01:50:51 jlec Exp $ - -EAPI=2 - -inherit toolchain-funcs multilib - -DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" -HOMEPAGE="http://samtools.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" - -LICENSE="MIT" -SLOT="0" -IUSE="examples" -KEYWORDS="~amd64 ~x86 ~x64-macos" - -src_prepare() { - sed \ - -e '/^CFLAGS=/d' \ - -e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \ - -e "s/-shared/& \$(LDFLAGS)/" \ - -i "${S}"/{Makefile,misc/Makefile} || die #358563 - sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die -} - -src_compile() { - emake CC="$(tc-getCC)" dylib || die - emake CC="$(tc-getCC)" || die -} - -src_install() { - dobin samtools || die - dobin $(find misc -type f -executable) || die - dolib.so libbam.so.1 || die - dosym libbam.so.1 /usr/$(get_libdir)/libbam.so || die - insinto /usr/include/bam - doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h || die - - doman ${PN}.1 || die - dodoc AUTHORS ChangeLog NEWS - - if use examples; then - insinto /usr/share/${PN} - doins -r examples || die - fi -} diff --git a/sci-biology/samtools/samtools-0.1.16.ebuild b/sci-biology/samtools/samtools-0.1.16.ebuild deleted file mode 100644 index a2181d1f6cfc..000000000000 --- a/sci-biology/samtools/samtools-0.1.16.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.16.ebuild,v 1.2 2011/07/18 01:50:51 jlec Exp $ - -EAPI=2 - -inherit multilib toolchain-funcs - -DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" -HOMEPAGE="http://samtools.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" - -LICENSE="MIT" -SLOT="0" -IUSE="examples" -KEYWORDS="~amd64 ~x86 ~x64-macos" - -src_prepare() { - sed \ - -e '/^CFLAGS=/d' \ - -e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \ - -e "s/-shared/& \$(LDFLAGS)/" \ - -i "${S}"/{Makefile,misc/Makefile} || die #358563 - sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die -} - -src_compile() { - emake CC="$(tc-getCC)" dylib || die - emake CC="$(tc-getCC)" || die -} - -src_install() { - dobin samtools || die - dobin $(find misc -type f -executable) || die - dolib.so libbam.so.1 || die - dosym libbam.so.1 /usr/$(get_libdir)/libbam.so || die - insinto /usr/include/bam - doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h || die - - doman ${PN}.1 || die - dodoc AUTHORS ChangeLog NEWS - - if use examples; then - insinto /usr/share/${PN} - doins -r examples || die - fi -} diff --git a/sci-biology/samtools/samtools-0.1.17.ebuild b/sci-biology/samtools/samtools-0.1.17.ebuild deleted file mode 100644 index dbdcbb777a18..000000000000 --- a/sci-biology/samtools/samtools-0.1.17.ebuild +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.17.ebuild,v 1.1 2011/07/18 01:50:51 jlec Exp $ - -EAPI=4 - -inherit multilib toolchain-funcs - -DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" -HOMEPAGE="http://samtools.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" - -LICENSE="MIT" -SLOT="0" -IUSE="examples" -KEYWORDS="~amd64 ~x86 ~x64-macos" - -src_prepare() { - sed \ - -e '/^CFLAGS=/d' \ - -e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \ - -e "s/-shared/& \$(LDFLAGS)/" \ - -i "${S}"/{Makefile,misc/Makefile} || die #358563 - sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die -} - -src_compile() { - emake CC="$(tc-getCC)" dylib || die - emake CC="$(tc-getCC)" || die -} - -src_install() { - dobin samtools $(find misc -type f -executable) - - dolib.so libbam.so.1 - dosym libbam.so.1 /usr/$(get_libdir)/libbam.so - - insinto /usr/include/bam - doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h - - doman ${PN}.1 - dodoc AUTHORS ChangeLog NEWS - - if use examples; then - insinto /usr/share/${PN} - doins -r examples - fi -} diff --git a/sci-biology/samtools/samtools-0.1.18-r1.ebuild b/sci-biology/samtools/samtools-0.1.18-r1.ebuild new file mode 100644 index 000000000000..30ae8d10d078 --- /dev/null +++ b/sci-biology/samtools/samtools-0.1.18-r1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.18-r1.ebuild,v 1.1 2013/01/23 10:51:13 jlec Exp $ + +EAPI=5 + +inherit multilib toolchain-funcs + +DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" +HOMEPAGE="http://samtools.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +IUSE="examples" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +src_prepare() { + sed \ + -e '/CC/s:=:?=:g' \ + -e "/LIBCURSES/s:=.*$:= $(pkg-config --libs ncurses):g" \ + -e '/^CFLAGS=/d' \ + -e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \ + -e "s/-shared/& \$(LDFLAGS)/" \ + -i "${S}"/{Makefile,misc/Makefile} || die #358563 + sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die + + tc-export CC +} + +src_compile() { + emake dylib + emake +} + +src_install() { + dobin samtools $(find misc -type f -executable) + + dolib.so libbam.so.1 + dosym libbam.so.1 /usr/$(get_libdir)/libbam.so + + insinto /usr/include/bam + doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h + + doman ${PN}.1 + dodoc AUTHORS ChangeLog NEWS + + if use examples; then + insinto /usr/share/${PN} + doins -r examples + fi +} -- cgit v1.2.3-65-gdbad